A key aim of biotechnology and nanotechnology is the construction of new biomaterials, including individual geometrical objects, nanomechanical devices, and extended constructions that permit the fabrication of intricate structures of materials to serve many practical purposes (Feynman et al., Miniaturization 282-296 (1961); Drexler, Proc. Nat. Acad. Sci. (USA) 78:5275-5278 (1981); Robinson et al., Prot Eng 1 295-300 (1987); Seeman, DNA & Cell Biol. 10:475-486 (1991); Seeman, Nanotechnol. 2:149-159 (1991)). Molecules of biological systems, for example, nucleic acids, have the potential to serve as building blocks for these constructions due to their self and programmable-assembly capabilities.
Nucleic acid molecules possess a distinct set of mechanical, physical, and chemical properties. From a mechanical point of view, nucleic acid molecules can be rigid (e.g., when DNA molecules are less than 50 nm, the persistent length of double stranded DNA (Bouchiat, C. et al., Biophys J 76:409-13 (1999); Tinland et al., Macromolecules 30:5763-5765 (1997); Toth et al., Biochemistry 37:8173-9 (1998)), or flexible. Physically, nucleic acid molecules are small, with a width of about 2 nanometers and a length of about 0.34 nanometers per basepair (e.g., B-DNA). In nature, nucleic acid molecules (i.e., RNA and DNA) can be found in either linear, double stranded or circular shapes. Chemically, DNA is generally stable, non-toxic, water soluble, and is commercially available in large quantities and in high purity. Unlike DNA, RNA is almost always a single-stranded molecule and has a much shorter chain of nucleotides. RNA contains ribose, rather than the deoxyribose found in DNA (there is a hydroxyl group attached to the pentose ring in the 2′ position whereas DNA has a hydrogen atom rather than a hydroxyl group). This hydroxyl group makes RNA less stable than DNA because it is more prone to hydrolysis. However, several types of RNA (tRNA, rRNA) contain a great deal of secondary structure, which help promote stability. In addition, RNA can be modified with various chemical modifiers known in the art to stabilize the molecules. Analogous molecules with modified backbones have been designed which change various characteristics of RNA, such as its instability to degradative enzymes. Some alternative antisense structural types are phosphorothioate, Morpholino, PNA (peptide nucleic acid), LNA (locked nucleic acid), TNA (treose nucleic acid) and 2′-O alkyl oligos. Some antisense structural types are being experimentally applied as antisense therapy, with at least one antisense therapy approved for use in humans.
Moreover, nucleic acid molecules are easily and highly manipulable by various well-known enzymes such as restriction enzymes, ligases and nucleases. Also, under proper conditions, nucleic acid molecules will self-assemble with complementary strands of nucleic acid (e.g., DNA, RNA, or Peptide Nucleic Acid, (PNA)). Furthermore, nucleic acid molecules can be amplified exponentially and ligated specifically. Thus, nucleic acid molecules are an excellent candidate for constructing nano-material and macro-material for use in biotechnology or medicine.
The concept of using nucleic acid molecules for non-genetic application has only recently emerged, such as in DNA-computation, where DNA are utilized in algorithms for solving combinatorial problems (Adleman, Science 266:1021-4 (1994); Guarnieri et al., Science 273:220-3 (1996); Ouyang et al., Science 278:446-9 (1997); Sakamoto et al., Science 288:1223-6 (2000); Benenson et al., Nature 414:430-4 (2001)), and DNA-nanotechnology, such as using DNA molecules for nano-scaled frameworks and scaffolds (Niemeyer, Applied Physics a-Materials Science & Processing 68:119-124 (1999); Seeman, Annual Review of Biophysics and Biomolecular Structure 27:225-248 (1998)). However, the design and production of DNA-based materials is still problematic (Mao et al., Nature 397:144-146 (1999); Seeman et al., Proc Natl Acad Sci USA 99:6451-6455 (2002); Yan et al., Nature 415:62-5 (2002); Mirkin et al., Nature 382:607-9 (1996); Watson et al., J Am Chem Soc 123:5592-3 (2001)). For example, nucleic acid structures are quite polydispersed with flexible arms and self-ligated circular and non-circular byproducts (Ma et al., Nucleic Acids Res 14:9745-53 (1986); Wang et al., Journal of the American Chemical Society 120:8281-8282 (1998); Nilsen et al., J Theor Biol 187:273-84 (1997)), which severely limits their utility in constructing DNA materials. Furthermore, the building blocks and motifs employed thus far are isotropic and multivalent, possibly useful for growing nano-scaled arrays and scaffolds (Winfree et al., Nature 394:539-44 (1998); Niemeyer, Applied Physics a-Materials Science & Processing 68:119-124 (1999); Seeman, Annual Review of Biophysics and Biomolecular Structure 27:225-248 (1998)), but not suitable for controlled growth, such as in dendrimer, or in creating a large quantity of monodispersed new materials, which are important to realize nucleic acid-based materials.
Other schemes of nano-construction using linear DNA molecules include a biotin-avidin based DNA network (Luo, “Novel Crosslinking Technologies to Assess Protein-DNA Binding and DNA-DNA Complexes for Gene Delivery and Expression” (Dissertation). Molecular, Cellular, and Developmental Biology Program, The Ohio State University (1997)), nanocrystals (Alivisatos et al., Nature 382:609-11 (1996)), DNA-protein nanocomplexes (Niemeyer et al., Angewandte Chemie-International Edition 37:2265-2268 (1998)), a DNA-fueled molecular machine (Yurke et al., Nature 406:605-8 (2000)), DNA-block copolymer conjugates (Watson et al., J Am Chem Soc 123:5592-3 (2001)), DNA-silver-wire (Braun et al., Nature 391:775-8 (1998)), and DNA-mediated supramolecular structures (Taton et al., Journal of the American Chemical Society 122:6305-6306 (2000)), DNA sensing via gold nanoparticles (Elghanian et al., Science 277:1078-81 (1997)), Y-shape DNA molecules (Eckardt et al., Nature 420:286 (2002)) and DNA patterning via dip-pen nanolithography (Demers et al., Science 296:1836-8 (2002)). However, the preceding prior art DNA-based structures are not suitable for large scale production and are further limited to linear DNA.
Matrixes formed from various polymers are important biomaterials useful in many biomedical applications, including controlled drug delivery and tissue engineering. Biomacromolecules including proteins are great precursors for novel hydrogels. For example, hydrogels made from peptides and proteins have already been recognized as smart materials (Petka et al., Science 281, 389 (1998); Zhang et al., J Am Chem Soc 127, 10136 (2005); J. Kisiday et al., Proc Natl Acad Sci USA 99, 9996 (2002); T. Amiya, T. Tanaka, Macromolecules 20, 1162 (1987); A. P. Nowak et al., Nature 417, 424 (2002); J. P. Schneider et al., J Am Chem Soc 124, 15030 (2002)), cell culture composition (S. Zhang et al., Biomaterials 16, 1385 (1995)) and artificial tissues (Lutolf et al., Nat Biotechnol 23, 47 (2005)).
However, there are still many limitations to protein hydrogels including the fact that the protein used is usually very expensive, the difficulty of designing and generating a primary amino acid sequence with a predictable structure, and the obvious immunogenecities of most proteins. Nucleic acid molecules, on the other hand, possess remarkable physical and chemical properties making it an ideal polymer. A large number of molecular tools also exist that can manipulate nucleic acid molecules at angstrom precision with enzymatic efficiency. For example, linear DNA was first used to construct an artificial nano-structure (Chen et al., Nature 350, 631 (1991)). Using “double crossover” DNA (two crossovers connecting two helical domains), a variety of geometric objects, periodic arrays and nanoscale mechanical devices have been constructed (Yan et al., Nature 415, 62 (2002); Yan et al., Science 301, 1882 (2003); Seeman, Trends Biochem Sci 30, 119 (2005); Pinto et al., Nano Lett 5, 2399 (2005)). Recently Lin et al. used a linear DNA molecule as a cross-linker to construct a thermal-stimulative polyacrylamide hydrogel, creating a DNA-polymer hybrid hydrogel system (Lin et al., J Biomech Eng 126, 104 (2004)). In addition, nucleic acid molecules have been conjugated with other chemical moieties, thus effectively linking diverse chemical functionalities (Zhu et al., J Am Chem Soc 125, 10178 (2003)).
A matrix structure or scaffold composed of synthetic nucleic acid molecules with or without any other chemical moieties has not been reported, which matrix would provide much better control in design and synthesis, higher biocompatibility, and better cost effectiveness. A key component for creating a nucleic acid matrix is cross-linkable nucleic acid monomers (building blocks), which cannot be realized by linear nucleic acid molecules. Branched and dendrimer-like DNA are known in the art (Y. Li et al., Nat Materials 3, 38 (2004); Li et al., Nat Biotechnol 23, 885 (2005)).
An important application for matrixes composed of nucleic acid molecules is controlled delivery of bioactive agents to a cell or organism. A major challenge in delivery of therapeutic agents is controlled temporal delivery of therapeutic agents (e.g., drugs or growth factors). Accordingly, it would be an advance in the art to provide controlled therapy that is free from undesirable complications ascribed to protein matrices. Furthermore, controlled drug delivery using chemical polymer compounds often results in batch to batch variance and is not reliably predictable with regards to pore size and geometrical pattern, thus not all issues have been completely resolved. In applications where a drug is incorporated into a degradable structure to control delivery, it is necessary to ensure that the degradation products of the structure do not interfere with the drug being delivered. Furthermore, it can be difficult to control the drug release rate by controlling the degradation process. For example, in cases where a porous polymer layer is used to hold drugs and/or to control the delivery rate, the delivery rate can depend sensitively on parameters of the porous layer (e.g., porosity, mean pore size, degradation rate) which are imperfectly controlled during fabrication. For example, two membranes made in different ways (or by different manufacturers) may have different drug delivery properties even if they nominally have the same pore size and porosity. Therefore, there is a need for new biomaterials, such as nucleic acid-based matrixes so as to provide a new and tremendous advantage in drug delivery, in vitro or ex vivo cell-based applications or therapies. In this regard nucleic acid-based matrices have yet to be successfully exploited.
Another important application of nucleic acid based matrixes is cell-free protein production. Nucleic acid-based matrixes have simply not been contemplated in the prior art, for utilization in cell-free protein production. The in vitro synthesis of proteins is an important tool for molecular biologists and has a variety of applications, including the rapid identification of gene products (e.g., proteomics), localization of mutations through synthesis of truncated gene products, protein folding studies, and incorporation of modified or unnatural amino acids for functional studies. The use of in vitro translation systems can have advantages over in vivo gene expression when the over-expressed product is toxic to the host cell, when the product is insoluble or forms inclusion bodies, or when the protein undergoes rapid proteolysis by intracellular proteases.
A substantial problem with recombinant systems is post-expression purification. Expressed recombinant proteins must be purified away from the entire host's lysates, which contain cell debris, lipids, carbohydrates, nucleic acids, and other proteins. It is still a great challenge to purify expressed proteins while keeping the protein activity high and the total cost down. In addition, there is a high cost and the danger associated with living organisms, e.g., production of toxins. Moreover, expensive media, serum, fermentaters, reactors, etc. are needed to maintain hosts. In addition, keeping batch to batch consistency for expressed recombinant protein within living organisms has proved to be difficult and expensive. Once a production process is established, it is almost impossible to improve it with living organisms, further increasing the final cost. Moreover, there also exists the danger of potential contamination by pathogen bacteria or viruses.
In practice, only a few cell-free systems have been developed for in vitro protein synthesis. In general, systems known in the art are derived from cells engaged in a high rate of protein synthesis. Such cell-free translation systems consist of extracts from rabbit reticulocytes, wheat germ and Escherichia coli. All are prepared as crude extracts containing all the macromolecular components (70S or 80S ribosomes, tRNAs, aminoacyl-tRNA synthetases, initiation, elongation and termination factors, etc.) required for translation of exogenous RNA. To ensure efficient translation, each extract must be supplemented with amino acids, energy sources (ATP, GTP), energy regenerating systems (creatine phosphate and creatine phosphokinase for eukaryotic systems, and phosphoenol pyruvate and pyruvate kinase for the E. coli lysate), and other co-factors (Mg2+, K+, etc.). There are two approaches to in vitro protein synthesis based on the starting genetic material: RNA or DNA. Standard translation systems, such as reticulocyte lysates and wheat germ extracts, use RNA as a template; whereas “coupled” and “linked” systems start with DNA templates, which are transcribed into RNA then translated.
RNA is transcribed from the DNA and subsequently translated without any purification. Such systems typically combine a prokaryotic phage RNA polymerase and promoter (T7, T3, or SP6) with eukaryotic or prokaryotic extracts to synthesize proteins from exogenous DNA templates. DNA templates for transcription:translation reactions may be cloned into plasmid vectors or generated by PCR. The “linked” system is a two-step reaction, based on transcription with a bacteriophage polymerase followed by translation in the rabbit reticulocyte lysate or wheat germ lysate. Because the transcription and translation reactions are separate, each can be optimized to ensure that both are functioning at their full potential. Conversely, many commercially available eukaryotic coupled transcription:translation systems have compromised one or both reactions so that they can occur in a single tube. Thus, yield is sacrificed for convenience.
Notably, the protein production systems in the prior are fundamentally limited solution-based systems. In addition, such solution based systems provide very limited production levels (e.g., yield of the protein of interest is at best about 750 μg/ml; Invitrogen). Indeed, none of the prior art systems utilize nucleic acid-based matrixes to produce proteins. Therefore, there is a clear need for an efficient and robust cell-free protein production system.
Therefore there is a need for new biomaterials that have applications in diverse areas of biotechnology and medicine. The present invention provides compositions and methods that provide nucleic acid-based matrixes useful in biotechnology and medicine.